Ken Prehoda <kenp at nmrfam.wisc.edu> writes:
>Since protein folding is believed to be thermodynamically controlled
Errr... NOT!
>(OK, see Agard, et al. for counterviews), this is really irrelevant
>to what you seem to be getting at. Remember that G is a state function
>and is therefore independent of path.
The bottom line is that folding pathway(s) is/are almost certainly
involved in getting to the _native_ state - so kinetics _are_
important.
I would bet money that anyone who says different is wrong!
As for the original point about the relatiave importance of secondary
vs tertiary vs intrinsic interactions, for controlling formation of
(secondary) structure:
Why can't they all be "equally" important??? That is, maybe in
one bit of a protein, intrinsic preferences are crucial for
driving structure formation, whereas in a different bit, secondary
interactions could be dominant.
If this was true, then there would be different percentages
of residues whose conformation was mainly determined by one of
the above "things". What these numbers would be is anyone's guess.
But, it is worth remembering that the so-called "hydrophobic effect"
is most likely to be the major driving force in structure formation.
In the simplest model for considering this effect, there need be no
difference between secondary and tertiary interactions when considering
this "effect".
My guess is that, on average, secondary and tertiary interactions of
residues dominate over "intrinsic" residue preferences" in driving the
formation of secondary structure.
_________________________________________________________________________
|| ,_ o Simon M. Brocklehurst,
| / //\, Oxford Centre for Molecular Sciences,
| \>> | Department of Biochemistry, University of Oxford,
| \\, Oxford, UK.
| E-mail: smb at bioch.ox.ac.uk|________________________________________________________________________